def main():
global recipes, user_path, main_path, desktop_path, code_path, KFV_path, KFP_path, excel_path_recover, excel_path, excel_path_test
print('Demo mode: ' + str(demo_mode))
if demo_mode == False:
# Read the excel file from the run and obtain the dictionary of samples
xls = pd.ExcelFile(excel_path)
code_data = pd.read_excel(xls, xls.sheet_names[2])
code_data = code_data.iloc[1:]
# generate listed dictionary for sampled plates
f = dict()
for i, key_row in enumerate(code_data['Table 1'].tolist()):
for idx, value in enumerate(code_data.iloc[i][1:]):
f.update({key_row + str(idx + 1): value})
thermocycler_values = pd.DataFrame(f, index=[0]).transpose()
# count number of declared elements in Dictionary to check with user declared values
num_samples_control = 0
for elem in f.values():
if elem != 0:
num_samples_control += 1
else:
excel_path = excel_path_test
xls = pd.ExcelFile(excel_path)
code_data = pd.read_excel(xls, xls.sheet_names[2])
code_data = code_data.iloc[1:]
# generate listed dictionary for sampled plates
f = dict()
for i, key_row in enumerate(code_data['Table 1'].tolist()):
for idx, value in enumerate(code_data.iloc[i][1:]):
f.update({key_row + str(idx + 1): value})
thermocycler_values = pd.DataFrame(f, index=[0]).transpose()
# count number of declared elements in Dictionary to check with user declared values
num_samples_control = 0
for elem in f.values():
if elem != 0:
num_samples_control += 1
print('Num muestras test: ' + str(num_samples_control))
# Get sample data from user
control = False
while control == False:
num_samples = int(
input('Número de muestras a procesar (excluidos PC + NC): '))
if (num_samples > 0 and num_samples <= 94):
control = True
else:
print(
'Número de muestras debe ser un número entre 1 y 94 (no incluyas los controles)'
)
print(
'------------------------------------------------------------------------'
)
print('El número de muestras registradas en el excel es: ' +
str(num_samples_control))
if num_samples_control != num_samples:
print(
'Error: El número de muestras entre excel y reportado no coincide, revisar por favor.'
)
exit()
else:
print('El número de muestras coincide')
print(
'------------------------------------------------------------------------'
)
# Get technician name
control = False
while control == False:
tec_name = '\'' + (input('Nombre del técnico (usuario): ')) + '\''
print(
'------------------------------------------------------------------------'
)
if isinstance(tec_name, str):
tec_name = tec_name.upper()
control = True
else:
print('Introduce tu usuario HUC, por favor')
# Get run session ID
control = False
while control == False:
id = (input('ID run: '))
print(
'------------------------------------------------------------------------'
)
try:
id = int(id)
except:
print('Por favor, assigna un ID numérico para este RUN')
if isinstance(id, int):
control = True
# Get date
fecha = datetime.now()
t_registro = '\'' + fecha.strftime("%m/%d/%Y, %H:%M:%S") + '\''
h_registro = fecha.strftime("%H:%M")
dia_registro = fecha.strftime("%Y_%m_%d")
# select the type of protocol to be run
[protocol, protocol_path] = select_protocol_type(KFV_path, KFP_path)
print(
'------------------------------------------------------------------------'
)
num_samples_c = math.ceil(
num_samples /
8) * 8 # corrected num_samples value to calculate needed volumes
num_cols = math.ceil(num_samples_c / 8)
final_data = generate_recipe(protocol, num_samples_c, recipes, num_samples)
print(final_data)
operation_data = {
'$technician': str(tec_name),
'$num_samples': str(num_samples),
'$date': str(t_registro),
'$run_id': str(id),
'$hora': str(h_registro),
'$dia': str(dia_registro),
'$num_s_corrected': str(num_samples_c),
'$num_cols': str(num_cols),
'$MMIX': str(final_data['MMIX'][0]),
'$Taqpath': str(final_data['Taqpath'][0]),
'$Assay': str(final_data['Assay'][0]),
'$Water': str(final_data['Water'][0])
}
#determine output path
run_name = str(dia_registro) + '_OT' + str(id) + '_' + protocol
final_path = os.path.join(main_path, run_name)
# create folder directory in case it doesn't already exist and copy excel registry file there
if not os.path.isdir(final_path):
os.mkdir(final_path)
os.mkdir(final_path + '/scripts')
os.mkdir(final_path + '/results')
thermocycler_values.to_excel(final_path + '/results/' + run_name +
'_thermocycler.xlsx',
index=True,
header=False)
os.mkdir(final_path + '/logs')
os.system('cp ' + excel_path + ' ' + final_path + '/OT' + str(id) +
'_samples.xlsx') # copy excel input file to destination
#reset desktop excel file
os.system('cp ' + excel_path_recover + ' ' + desktop_path +
'fill.xlsx')
if protocol == 'V':
os.system('cp ' + main_path +
'covid19huc/Automation/volumes_viral_readme.html' + ' ' +
final_path + '/readme.html')
pV = generate_multi_well_viral(final_path + '/results', final_data)
mini_well = generate_multi_mini_well(final_path + '/results',
final_data, protocol)
update_readme(final_path, 'readme.html', protocol, [pV, mini_well],
operation_data)
elif protocol == 'P':
os.system('cp ' + main_path +
'covid19huc/Automation/volumes_pathogen_readme.html' +
' ' + final_path + '/readme.html')
pB = generate_multi_well_pathogen_IC(final_path + '/results',
final_data)
pR = generate_multi_well_pathogen_R(final_path + '/results',
final_data)
mini_well = generate_multi_mini_well(final_path + '/results',
final_data, protocol)
update_readme(final_path, 'readme.html', protocol,
[pR, pB, mini_well], operation_data)
else:
print('BEWARE! This protocol and ID run already exists! Exitting...')
exit()
# move protocol .py files to final destination
for file in os.listdir(protocol_path): # look for all protocols in folder
if file.endswith('.py'):
position = re.search(
'_template',
file).start() # find _ position after the name and get value
filename = file[:position] + '_' + str(dia_registro) + '_OT' + str(
id) + '.py' # assign a filename date + station name + id
os.system('cp ' + os.path.join(protocol_path, file) + ' ' +
os.path.join(final_path + '/scripts/', filename))
# change values to protocols for final user
for filename in os.listdir(final_path + '/scripts/'):
if re.match('KA', filename):
update_files(final_path, filename, final_data, operation_data)
elif re.match('KB', filename):
update_files(final_path, filename, final_data, operation_data)
elif re.match('KC', filename):
update_files(final_path, filename, final_data, operation_data)
else:
print('No files found')
def main():
global recipes, user_path, main_path, desktop_path, code_path, KFV_path, KFP_path, excel_path_recover, excel_path, excel_path_test
print('Demo mode: ' + str(demo_mode))
if demo_mode == False:
# Read the excel file from the run and obtain the dictionary of samples
[num_samples_control,
thermocycler_values] = thermocycler_generator(excel_path)
else:
excel_path = excel_path_test
[num_samples_control,
thermocycler_values] = thermocycler_generator(excel_path)
print('Num muestras test: ' + str(num_samples_control))
# Get sample data from user
control = False
while control == False:
num_samples = int(
input('Número de muestras a procesar (excluidos PC + NC): '))
if (num_samples > 0 and num_samples <= 94):
control = True
else:
print(
'Número de muestras debe ser un número entre 1 y 94 (no incluyas los controles)'
)
print(
'------------------------------------------------------------------------'
)
print('El número de muestras registradas en el excel es: ' +
str(num_samples_control))
if num_samples_control != num_samples:
print(
'Error: El número de muestras entre excel y reportado no coincide, revisar por favor.'
)
exit()
else:
print('El número de muestras coincide')
print(
'------------------------------------------------------------------------'
)
# Get technician name
control = False
while control == False:
tec_name = '\'' + (input('Nombre del técnico (usuario): ')) + '\''
print(
'------------------------------------------------------------------------'
)
if isinstance(tec_name, str):
tec_name = tec_name.lower()
tec_name = tec_name[0].upper() + tec_name[1:]
control = True
else:
print('Introduce tu usuario HUC, por favor')
# Get run session ID
if demo_mode == True:
id = 1000001
fecha = datetime.now()
t_registro = '\'' + fecha.strftime("%m/%d/%Y, %H:%M:%S") + '\''
h_registro = fecha.strftime("%H:%M")
dia_registro = fecha.strftime("%Y_%m_%d")
else:
if not os.path.isdir(id_path):
os.mkdir(id_path)
id_runs = id_path + '/id_runs.txt'
with open(id_runs, 'w') as f:
f.write('ID\tdate\thora\tsample_num\n')
f.close()
if os.path.isdir(id_path):
# Get date
id_runs = id_path + '/id_runs.txt'
fecha = datetime.now()
t_registro = '\'' + fecha.strftime("%m/%d/%Y, %H:%M:%S") + '\''
h_registro = fecha.strftime("%H:%M")
dia_registro = fecha.strftime("%Y_%m_%d")
with open(id_runs, 'r+') as f:
lines = f.read().splitlines()
last_line = lines[-1]
if last_line.split('\t')[0] == 'ID':
id = 1
print('The ID for the run will be: ' + '%d' % id +
', on ' + dia_registro + ' ' + h_registro + '\n')
f.write('%d' % 1 + '\t' + dia_registro + '\t' +
h_registro + '\t' + '%d' % num_samples + '\n')
else:
id = int(last_line.split('\t')[0]) + 1
print('The ID for the run will be: ' + '%d' % id +
', on ' + dia_registro + ' ' + h_registro + '\n')
f.write('%d' % id + '\t' + dia_registro + '\t' +
h_registro + '\t' + '%d' % num_samples + '\n')
f.close()
# select the type of protocol to be run
[protocol, protocol_path] = select_protocol_type(KFV_path, KFP_path)
print(
'------------------------------------------------------------------------'
)
num_samples_c = math.ceil(
num_samples /
8) * 8 # corrected num_samples value to calculate needed volumes
num_cols = math.ceil(num_samples_c / 8)
final_data = generate_recipe(protocol, num_samples_c, recipes, num_samples)
print(final_data)
operation_data = {
'$technician': str(tec_name),
'$num_samples': str(num_samples),
'$date': str(t_registro),
'$run_id': str(id),
'$hora': str(h_registro),
'$dia': str(dia_registro),
'$num_s_corrected': str(num_samples_c),
'$num_cols': str(num_cols),
'$MMIX': str(final_data['MMIX'][0]),
'$Taqpath': str(final_data['Taqpath'][0]),
'$Assay': str(final_data['Assay'][0]),
'$Water': str(final_data['Water'][0])
}
#determine output path
run_name = str(dia_registro) + '_OT_' + str(id) + '_' + protocol
if demo_mode == True:
run_name = run_name + '_prueba'
final_path = os.path.join(main_path, run_name)
# create folder directory in case it doesn't already exist and copy excel registry file there
if not os.path.isdir(final_path):
os.mkdir(final_path)
os.mkdir(final_path + '/scripts')
os.mkdir(final_path + '/results')
thermocycler_values.to_excel(final_path + '/results/' + run_name +
'_thermocycler.xlsx',
index=True,
header=False)
os.mkdir(final_path + '/logs')
os.system('cp ' + excel_path + ' ' + final_path + '/OT' + str(id) +
'_samples.xlsx') # copy excel input file to destination
#reset desktop excel file
os.system('cp ' + excel_path_recover + ' ' + desktop_path +
'fill.xlsx')
if protocol == 'V':
os.system('cp ' + main_path +
'covid19huc/Automation/volumes_viral_readme_linux.html' +
' ' + final_path + '/readme.html')
pV = generate_multi_well_viral(final_path + '/results', final_data)
mini_well = generate_multi_mini_well(final_path + '\\results',
final_data, protocol,
num_cols)
update_readme(final_path, 'readme.html', protocol, [pV, mini_well],
operation_data)
elif protocol == 'P':
os.system(
'cp ' + main_path +
'covid19huc/Automation/volumes_pathogen_readme_linux.html' +
' ' + final_path + '/readme.html')
pB = generate_multi_well_pathogen_IC(final_path + '/results',
final_data)
pR = generate_multi_well_pathogen_R(final_path + '/results',
final_data)
mini_well = generate_multi_mini_well(final_path + '\\results',
final_data, protocol,
num_cols)
update_readme(final_path, 'readme.html', protocol,
[pR, pB, mini_well], operation_data)
else:
print('BEWARE! This protocol and ID run already exists! Exitting...')
exit()
# move protocol .py files to final destination
for file in os.listdir(protocol_path): # look for all protocols in folder
if file.endswith('.py'):
position = re.search(
'_template',
file).start() # find _ position after the name and get value
filename = file[:position] + '_' + str(dia_registro) + '_OT' + str(
id) + '.py' # assign a filename date + station name + id
os.system('cp ' + os.path.join(protocol_path, file) + ' ' +
os.path.join(final_path + '/scripts/', filename))
# change values to protocols for final user
for filename in os.listdir(final_path + '/scripts/'):
if re.match('KA', filename):
update_files(final_path, filename, final_data, operation_data)
elif re.match('KB', filename):
update_files(final_path, filename, final_data, operation_data)
elif re.match('KC', filename):
update_files(final_path, filename, final_data, operation_data)
else:
print('No files found')